For specialized purposes within detection of antigen-specific T cells ImmuMap offers analysis using the dCODE™ Dextramer platform. This innovative platform takes advantage of unique DNA barcodes enabling us to search for up to more than 1000 different T cell specificities in a single cell sample using fluorescence-based cell sorting and next-generation sequencing (NGS). This method is based on the use of DNA barcoded MHC complexes and has been developed and pioneered in the lab of our co-founder Professor at the Danish Technical University, PhD Sine Reker Hadrup. The technology is essentially an expansion to the common MHC multimer staining, see our site about MHC multimer staining for an explanation of this method. We believe we are unique in offering the use of DNA barcoded MHC complexes as a service to our commercial customers.
The dCODE™ Dextramer platform can be explained briefly as an initial standard staining of T cells with fluororescently-labeled peptide:MHC complexes followed by sorting of cells recognizing the peptide:MHC complex. This standard procedure is then followed by PCR amplification of the barcodes bound to the sorted cells and finally an NGS analysis. The dCODE™ Dextramers are, as common MHC multimers, built of a light chain, a heavy chain, a peptide and a fluorochrome-conjugated backbone. In addition, for each specificity the backbone has been labeled with a unique DNA barcode that can be sequenced and read by NGS.
All DNA barcoded MHC complexes are labelled with the fluorochrome PE and thus different T cell specificities cannot be elucidated from the flow staining alone. However, after sorting of the whole CD8+PE+ population we can identify the unique DNA barcode and consequently the specificity of the T cells in question by de-convoluting using next-generation sequencing and our own bioinformatics analysis platform.
The applicability of the dCODE™ Dextramer platform is huge within both immune-oncology for e.g. development of novel neoepitope-targeted therapies, and within the field of autoimmune diseases focused on elucidating the specificity of self-reacting T cells. In the immune-oncology field in recent years there has been an immense interest for targeting the so-called neoepitopes arising from patient-specific mutation antigens. This interest stems from convincing clinical data of neoepitope targeting approaches, and neoepitope targeting may be the perfect extra boost of the immune system for e.g. patients not responding to anti-PD1 or other checkpoint inhibitor antibodies. For elucidating the whole picture on existing T cell specificity in such patients the use of DNA barcoded MHC complexes is an obvious choice.
Current algorithms for predicting such neoepitopes from e.g. RNA sequencing data from tumor biopsies are, however, far from perfect, and hence there is a large, and until now, unmet need for a multi-specificity T cell response screening strategy. The DNA barcoded MHC complexes is a major achievement in order to solve this need. Within the autoimmune field less is known about the self-specific T cells and the dCODE™ Dextramer platform may be the shortcut needed to massively develop this field.
We currently offer analyses using DNA barcoded MHC complexes for human samples only, while we are working on establishing the method for mouse samples.
Contact our staff today for a discussion on how we can help you.
Reference: Bentzen, AK. et al. "Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes", Nature Biotechnology (2016)